Hmm. If I'm reading you right, then you ask some complicated questions CB. I don't wanna overcomplicate or confuse my answer so I'll just use a few examples.
The Ranger (or any human class) has built into it certain abilities at each level. Sometimes more than one. Like in AD&D, but none of the abilities are magical (except for Clerics and Monks and Hermits who get religious or spiritual capabilities, some of which might seem magical, but most are far more psychological, mental, or pragmatic), they are all skill based.
But at any point a Ranger (or the person playing them) can forego their normal "class skill set" (cause all skills have to be learned and trained at) for some skill possessed by another class (only a very few skills are restricted per se, but you still gotta get somebody to teach ya whatever it is you wanna learn) or just a general human skill.
This avoids "builds" and allows all human characters to be unique. A Ranger can be just like the standard idea of a Ranger as far as the class template goes, but at any point he can trade up or learn different skills, or even push around certain skills to be learned at an earlier or later time than would be the "norm" or standard class model. (The exception are some of the higher level skills, which require a lot of experience to master. For instance a 20th level Soldier gets Commander in Chief, which has many different advantages, and a 20th level Paladin gets Sainthood, which also gets more than one advantage type. Sainthood as an example gives spiritual, mental, social, cultural, and religious benefits, as well as bestowing the Sainthood skill set.) And you can expend intelligence and wisdom and other things to help with your training, to speed up, put off, or rearrange skill sets.
So it's like in the real world. A Soldier for instance must go through basic training, and there is a standard model for skills that must be learned and shared among all soldiers. After that they can differentiate, depending on specialty path, and they can train in things for both professional and personal reasons. (A soldier can learn to play the guitar and sing well, like a Bard, not because it's part of his professional skill set, but because he wants to and finds it useful in other ways.) And while one Special Forces Soldier (to use a real world analogy) learns advanced communications as a lieutenant, another might as a sergeant. Or he might never learn advanced communications. He may learn basic bomb disposal instead. Is this making sense? So it works like that. A Ranger is a Ranger and all Rangers must know somethings in common. After that there is wide variation.
But there are no "builds." Each build or variation is unique. Fro instance if a Ranger is primarily a Frontier's lawman, scout, and man, (and most are in my setting) then he's probably gonna wanna know the languages of the frontier, and some Persian. If he works as an undercover operative in Constantinople, he'll wanna know Greek and Latin, and some trade languages. If he's along the frontiers he's gonna wanna know how to handle fires and disasters. In Constantinople he'll wanna know how to handle plagues and diplomacy.
So what a Ranger does and what skills sets he knows will be primarily dependent upon where he is located, what he's likely to run into, and when, who he's dealing with, what languages are being spoken, and what his job will entail. It will also be dependent on the individual. If a Ranger wants to know how to play an instrument like a Bard, pray or write sermons like a Cleric, or lead a small group like a Soldier, then he can learn those things if he can find somebody to teach him.
Now, let me see if I can give a few brief specific responses.
So, you have an actual 'Fire Fighting' skill representing skill at putting out fires? What does the 'Handle Disaster' skill do for you? Why is this a different skill than some sort of generalized, 'Manage and Organize Groups' or 'Knows about Logistics' skill?
It depends a lot on the nature of the disaster. It could be organizing groups, taking charge, or it could be triage, or Search and Rescue, or it could be reconnaissance and sizeup (recognizing what needs to be done and in what order). It could be all of these things. It could be an earthquake, a major storm, a wildfire, a plague, a surprise invasion on a defenseless area. I guess I should explain that some skills in my game are really "Skill Sets" and are far more complicated than a single skill. For most purposes handling ropes is a skill, Handling Disaster is a situationallly dependent "skill-set." I let the player decide how they will handle their skill sets, and in what order of response.
Why did you choose to treat 'Deal with Plague' as being different than a generalized 'Knows about Medicine' skill?
Because a plague is very different from what one normally encounters in common medical situations, and yet were common enough and lethal enough in the ancient world to be a real problem requiring real skill to respond to. Complicated skill sets usually depend on need, response, and how likely you are to encounter that situation.
How many skills do have and how do you handle issues like skill overlap (two skills are described in such a way that either could apply), skill gaps (some activity is not covered by one of your skills), and allocation of skills into your buckets such that everyone seems skillful (lots of buckets but not alot of points to fill them with)?
As many skills as there are in real life. It works just like real human skills in this way. I've written up a lot of skills but if a player can suggest one and we don't have it, and he wants it, I (or sometimes we) will sit down and write it up. It has to be appropriate to the setting and actually useful enough that the player might need it. Fro instance digging a well, anybody fit enough and who has enough time and the right tools, can do. Locating water, that's a skill.
Some skills obviously overlap. A Soldier and a Ranger will both know how to fight well. Conduct ambushes, etc. The way they go about it will vary. Depends on training and intent. A Soldier is far more likely to know how and to be good at group ambushes, ambushing parties and combined forces. A Ranger in my setting will be better at ambushing individuals, or small groups. Cause that's what Soldiers tend to do, ambush groups, and Rangers tend to ambush individuals. Again, like real life. Same skill, different applications.
Don't usually use points for skills either. You usually prove you possess a skill by describing and/or acting out exactly how you'd do a thing. Dice are usually only introduced at the player's discretion and/or if a thing is really, really difficult and you are is attempting something at the very limits of human capability or physical ability, or if some force is opposing your attempt to use a skill.
I think I've probably already explained above how characters get and use and arrange their skills. Core, then whatever they wish to do. If people have skill gaps, then usually the party can cover it, or if no-one in the party is trained for it they can still attempt it based on their closest skill or skill set. It's like in real life. Having a skill at archery does not exclude being able to start a fire. You may not be trained at starting fires, but you can still attempt it. Just using good old human ingenuity, observation, and experimentation. Skills aren't exclusionary, they just aren't necessarily applicable to any given situation.
I should also say that in my settings players can transfer their real world skills (assuming they are setting appropriate - a Cleric of the 9th century doesn't know and has no need for computer hacking skills) to their character. And practice them in-game.
I didn't think you were implying that, but as someone with my own somewhat customized skill list I'm always interested in how someone else approached the challenge without falling into some of the traps of GURPS on one end and 4e on the other.
I'm not sure exactly what traps ya mean. But I don't think we overcomplicate it. It works more like real life skills. I want it to be flexible, but we don't overmath it up or lay on complicated rules or strictures.
Explorers have access to skills like Diplomacy, Boating, Navigation, Survival, Use Rope, Climb, Run, Porter, Swim, Spot, and so forth - all of which are basically 'mundane' skills in as much as they are intended over a range of low level characters to reflect what real people can actually do. On the other hand, in the case of Climb and Run and perhaps even Swim, sufficient skill in those would let you do 'superhuman' things along the lines of the 'jump 20' up' that you site.
In this setting (Terra), since everybody's human, unless they are an invader or visitor, no-one can jump twenty feet straight up. Biology and physics limits it. So obviously, given that caveat, our situations and settings differ.
Now in the sea setting, it will be different. Sometimes things like you say will occur, it will depend on the situation, and who is doing what. For instance an Elf using magic or some power might very well leap 20 feet upwards. Even a human affected or using magic could do so possibly. In Terra though actions are limited to what humans can actually do based on highest skill and physical and mental and psychological development. So in Terra development and training is the key to accomplishment. There is no magic there, though occasionally miracles occur. Like religious miracles.
I like the idea of an Explorer class by the way. As a separate class. I like Explorers. In the real world. Those are guys with a wide Ranger of impressive and very useful skill sets. they are often also survivalists extraordinaire.
I will say this in general about skill use in many games. As a sort of theoretical sidenote. I think there was a mistaken game design principle of taking skills and skill sets and then reverse engineering them to fit onto and act like powers and other capabilities in games, thereby creating unrealistic and feats which are really just minor magical powers. This really makes skills indistinguishable from other capabilities in my opinion. And either degrades or erases their true value.
So the basic idea in design was to take game background assumptions and then add on skills and skill sets so that skills don't remain skills at all but evolve into other things. In other words game assumptions first, then just plug in skills as an extra "power." This isn't how skills actually work. Skills are trained abilities that develop and evolve with practice and experience, they never exceed certain real limitations, but the combination of a high degree or training and experience, combined with multiple skills and skill sets are the things that make humans so amazingly versatile, capable, and accomplished. It's not that skills are magic, or should act like magic, it's that when you are properly trained and able, you can do seemingly miraculous things. Things other people might think impossible, not because they really are impossible, but that you are skilled enough to overcome the impossible. But with many games, they got the equation backwards (and this is why I think skills are inadequate in many games, overcomplicated in some games, useless in some, and just plain kinda silly and unbelievable in others). They started with game assumptions first, then just tacked on skills as an afterthought. I started first with the actual nature of skills (something I've both studied and practiced for a long time), then wrote the game assumptions around that. Individual skills are naturally limited, but used properly and in the correct combinations, skills are like a human version of near God-like capabilities. For skills are in many ways the nature of Genius and accomplishment. A kind of miracle that is both mundane, yet incredible at the same time.
Well, I gotta go check my books and work out now.
Hope I answered your questions.
Gave it a shot anyways.
See ya.